Compress vs Uncompress when managing blend files with GIT
Back to your title's question: 

Compress vs Uncompress file into version control system?

Use compressed if the system can not create a differential
Most version control systems have their own compress algorithm when storing each file.
Using Blender's compression will only confuse the system on file content and unable to find a minimum diff between different versions of files which may lead to massive amount of savings in your repository.
While some systems using .gz or other common compression methods, .blend files are most likely treated as binary files unless there is a toolchain to let the system decode the meaning of Blender's files. So an uncompressed .blend  might be treated as a compressed one, then choose the smaller one since Blender's compression is specifically to it's own file type.